ENCD-6124-treatment-negative-value

src/encoded/schemas/changelogs/treatment.md

@@ -1,5 +1,8 @@
 ## Changelog for treatment.json
 
+### Schema version 14
+* Restricted *amount* and *duration* properties to have a minimum value of 0.
+
 ### Schema version 13
 * Modified regex pattern for *product_id* to disallow blank strings.
 

src/encoded/schemas/treatment.json

@@ -28,7 +28,7 @@
     },
     "properties": {
         "schema_version": {
-            "default": "13"
+            "default": "14"
         },
         "documents": {
             "description": "Documents that describe the treatment protocol."
@@ -50,7 +50,8 @@
         },
         "amount": {
             "title": "Amount",
-            "type": "number"
+            "type": "number",
+            "minimum": 0
         },
         "amount_units": {
             "title": "Amount units",
@@ -76,7 +77,8 @@
         },
         "duration": {
             "title": "Duration",
-            "type": "number"
+            "type": "number",
+            "minimum": 0
         },
         "duration_units": {
             "title": "Duration units",

src/encoded/tests/fixtures/schemas/treatment.py

@@ -149,3 +149,16 @@ def treatment_12(testapp):
         'treatment_term_id': 'CHEBI:23965'
     }
     return testapp.post_json('/treatment', item).json['@graph'][0]
+
+
+@pytest.fixture
+def treatment_with_negative_duration_amount_units(testapp, organism):
+    item = {
+        'treatment_term_name': 'ethanol',
+        'treatment_type': 'chemical',
+        'duration': -9,
+        'duration_units': 'day',
+        'amount': -100,
+        'amount_units': 'mg'
+    }
+    return item

src/encoded/tests/test_upgrade_treatment.py

@@ -78,3 +78,14 @@ def test_treatment_upgrade_12_13(upgrader, treatment_12):
     value = upgrader.upgrade('treatment', treatment_12, current_version='12', target_version='13')
     assert value['schema_version'] == '13'
     assert 'product_id' not in value
+
+
+def test_treatment_upgrade_13_14(upgrader, treatment_with_negative_duration_amount_units):
+    value = upgrader.upgrade('treatment', treatment_with_negative_duration_amount_units, current_version='13', target_version='14')
+    assert value['amount'] == 0
+    assert value['duration'] == 0
+    assert value['notes'] == (
+        'This treatment erroneously had a negative amount of -100 '
+        'and was upgraded to 0. This treatment erroneously had a '
+        'negative duration of -9 and was upgraded to 0.'
+    )

src/encoded/upgrade/treatment.py

@@ -112,3 +112,26 @@ def treatment_12_13(value, system):
     # https://encodedcc.atlassian.net/browse/ENCD-6102
     if 'product_id' in value and value['product_id'] == '':
         value.pop('product_id')
+
+
+@upgrade_step('treatment', '13', '14')
+def treatment_13_14(value, system):
+    # https://encodedcc.atlassian.net/browse/ENCD-6124
+    if value.get('amount') < 0:
+        current_notes = ''
+        if 'notes' in value:
+            current_notes = value['notes']
+        value['notes'] = (
+            f'{current_notes} This treatment erroneously had a negative'
+            f' amount of {value["amount"]} and was upgraded to 0.'.strip()
+        )
+        value['amount'] = 0
+    if value.get('duration') < 0:
+        current_notes = ''
+        if 'notes' in value:
+            current_notes = value['notes']
+        value['notes'] = (
+            f'{current_notes} This treatment erroneously had a negative'
+            f' duration of {value["duration"]} and was upgraded to 0.'.strip()
+        )
+        value['duration'] = 0